Interpreting the Phenotype Summary in Allele Details
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This help document describes the Phenotypes section of an Allele Detail report and answers the following questions:

See also:

What is the purpose of the Phenotypes section?

The purpose of the Phenotypes section is to display all genotypes involving an allele with annotations in affected anatomical systems. In this table, you can:

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How do I interpret the Phenotypes section?

Note: The Phenotypes section begins with a Key that explains the abbreviations used in this section, the Allelic Composition, Genetic Background and Cell Lines associated with each Genotype containing the featured allele. These are followed by a matrix of the Affected Systems examined for the genotypes.

Key: genotypes, colors, and symbols

The key at the top of the Phenotype Summary by Mammalian Phenotype terms table contains one color bar for each different allelic "state" (e.g., homozygous, heterozygous). Each state has a color, an abbreviation for the state (e.g., hm for homozygous, ht for heterozygous, and so on) and a number (arrayed sequentially) for each search result.

hm   (orange)homozygous
ht   (blue)heterozygous
cn (green)conditional genotype
cx   (purple)complex (more than one genome feature)
tg    (pink)involves transgenes
ot  (brown)other: hemizygous, indeterminate...
NNormal phenotype. Current annotations for this genotype and term indicate absence of abnormality.
NOT a model for this disease, contrary to expectation. See References for details.
There is an abnormal phenotype in the affected system. Click ► in the Affected Systems column to see the specific column annotated. Click the term name to view it in the Mammalian Phenotype Browser.
Blank spaceNo information.
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Key: numbers

There is a number for each genotype involving this allele with annotations in affected anatomical systems. Numbers increase sequentially. If the number of genotypes in MGI involving this allele is 29, there will be 29 rows in the Key table (e.g., hm1...ht15...cx20...tg29) and 29 columns in the Affected Systems table.

Genotype Genotype abbreviation (e.g., hm1, ht4) used in this web page.
Allelic CompositionGenotype of each allele, linked to its MGI Allele Detail report.
Genetic BackgroundMouse strains involved, if known.
Cell Line(s)Cell line(s)

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Affected Systems

The Affected Systems column lists anatomical terms from the Mammalian Phenotypes Browser for which there are phenotypic annotations.

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Show or hide all annotated terms

showClick to expand or open a view of all annotations for this allele.
hideClick to contract or close the annotation list.

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Links

To see information for all check marked anatomical terms in a column (i.e., all the Affected Systems for hm1):

Click View phenotypes for all genotypes (concatenated display) to see all genotypes and phenotypic annotations in a single browser window.

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What should appear in the Sex row?

For genotypes with sex specific data, the appropriate male or female symbol appears, indicating the phenotypic sex analyzed. If this row is missing, either sex specific data were not reported or there were no sex differences.

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What should appear in the Source row?

When one of the genotypes has data from one of the high-throughput phenotyping projects, the curation source is displayed for all genotypes. WTSI (Wellcome Trust Sanger Institute) and EuPh (Europhenome Mouse Phenotyping Resource) are examples. If this row is missing, MGI is the curation source.

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What should appear on the Affected Systems list? How is it sorted?

The Affected Systems list contains annotation terms from the Mammalian Phenotypes Browser. If a term does not appear, it means that, at this time, the MGI database does not contain annotations for this allele to the term. The sort order in the summary table is always alphabetical (e.g., behavioral/neurological before cardiovascular, skeleton before skin/coat/nails).

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What's the difference between N and ∅;? What does a blank cell indicate?

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Where is the research that supports an annotation?

Click the column header in the Genotypes row (e.g., hm1, ht15, cx19). In the window that appears, J-numbered citations (e.g., J:7454) appear after each Mammalian Phenotype Browser term (in parentheses). Clicking a citation brings up its MGI References report. Here you will find publication details, an abstract, and links to additional MGI information.

When there is more than one reference paper, bullet items beneath the Mammalian Phenotype vocabulary terms differentiate which paper goes with which note.

Bullet items provide additional information about the phenotype and may or may not be present, regardless of the number of papers.

Note: There is also a References section at the bottom of the Phenotypic Allele Detail report. Clicking All references displays links to all citations associated with the allele. Matching items are sorted chronologically with the most recent papers appearing at the top.

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More questions

Can I see annotations for every checkmarked item in a Genotypes column?

Yes. Click the colored box at the head of the Genotypes row (i.e., hm1, ht4). A new window appears, containing all available phenotypic details by genotype.

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How many new windows can I open?

As many as desired.

Clicking any of the numbered genotypes opens a new window.
Note: Each click will open a new window in front of your current browser window.

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What else is there to know about genotype windows?

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What if I'm only interested in disease models?

Scroll down the Allele Detail report to the Disease Models section. A check mark appears in any Genotypes column where there is phenotypic evidence of a disease model. Click the colored box at the top of that column (e.g., cn1) to access phenotypic details.

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How do I get rid of extra windows, headers, or subsystem views?

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Why aren't all the systems in the Mammalian Phenotype vocabulary listed?

Only those systems with at least one annotation appear in the table.

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How can I tell, without opening every window, what alleles and strains are involved with all genotypes?

Scroll down to below the Affected Systems table and click the link to View phenotypes for all genotypes (concatenated display). All genotypes listed in the Phenotypes section appear, paired with their allelic composition and genetic background data. The view of the genotype data is vertical rather than horizontal (as in the Affected Systems table).

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Why is the order of systems different in the summary table versus the genotype detail table?

Items in the Affected Systems list on the Phenotypes table are ordered alphabetically.

For any annotated subterms beneath these systems, the order is weighted by importance as specified by MGI curators.

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How often are annotations added?

MGI curators add new annotations from the literature every day. The MGI web site is updated with these and other new data once a week.

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Are there examples?

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